Here is my CV - Department of Chemistry and Biochemistry

Department of Chemistry & BiochemistryUniversity of California, Santa BarbaraCHUN WU , PHD (CHEMISTRY) MS (COMPUTER SCIENCE)Santa Barbara, CA 93106Tel: (805) 280-6645Fax: (805) 893-8170koolben5@gmail.comEducationhttp://www.chem.ucsb.edu/~cwu/University of Delaware Analytical Chemistry Ph.D. (GPA 3.798/4) 2005Computational biophysical chemistry research(Advisor: Yong Duan)Computer Science M.S. (GPA 3.770/4) 2005Xiamen University Analytical Chemistry M.S. 1999(Advisor: Yaoqun Li)Chemistry B.S. 1995Scholarships and AwardsTravel stipend from the IBBI conference (Isolated Biomolecules and Biomolecular Interactions), Berlin (2010)Travel stipend from the Gorden research conference: Biological Molecules in Gas Phase and in Solution (2009)Named to the Dean’s list in recognition of Scholastic Excellence (top 10%), University of Delaware (2004)Excellent Thesis (top 5 %), Chemistry Department, Xiamen University (1999)No. 1 (~60 applicants), the entrance exams, analytical chemistry graduate program, Xiamen University (1995)Excellent graduation research paper (top 5%), Chemistry Department, Xiamen University (1995)Excellent sport achievement, Chemistry Department, Xiamen University (1993)Research Experience2011-nowAssistant Research/Research Assistant Professor, Chem. and Biochem. UC Santa BarbaraFolding of intrinsically disordered hormone peptides (the calcitonin family and Incretins), Binding ofhormone peptides to receptors, Inter-domain motion of chemotaxis protein CheA, Force fielddevelopment (membrane lipid and implicit solvent protein models), GPU computing2008-2011 Assistant Specialist, Chemistry and Biochemistry, University of California, Santa Barbara2007-2008 Postdoc Researcher, Chemistry and Biochemistry, University of California, Santa BarbaraAdvisors: Prof. Joan E. Shea & Prof. Michael T. Bowers“Pathologic Protein Folding and Human diseases” : folding and oligomerization of amyloiddisease-relatedproteins (amylin of type II diabetes, amyloid-β peptides of Alzherimer’sdisease, prion protein fragment of “mad cow” disease); amyloid fibril-dye binding; folding ofsmall fast folding α/β proteins (all-atom molecular simulations, Ion-mobility massspectrometry, CD spectroscopy)2005-2007 Postdoc Researcher, University of California Davis, Genome Center, DavisAdvisor: Prof. Yong DuanAll-atom simulation of amyloid fibril formation and inhibition (amylin fragment of type II diabetes,yeast prion protein Sup35 fragment of mad cow disease) and protein folding simulations,protein/ligand force field development, MPI parallel implementation of simulation codes,development of protein modeling tools1999-2005 PhD Student, Computational Biochemistry, University of DelawareAdvisor: Prof. Yong DuanDissertation: “Nucleation and growth of an amyloidogenic hexapeptide (NFGAIL) of type IIdiabetes in aqueous solution observed in molecular dynamics simulations”1996-1999 MS Student, Analytical chemistry, Xiamen UniversityAdvisor: Prof. Yaoqun LiDevelopment of FPATH --a software package used by the lab-built spectrometer to realize theoptimum scanning route for non-linear variable-angle synchronous fluorescence (NLVASF); UsingFPATH-enabled NLVASF to measure complex biological and environmental samplesReviewing & affiliationReviewer:European Research Council/ERC starting grant1

Curriculum VitaeChun WuNature Chem., J Am Chem Soc, J Mol Biol, Biophys J, J Phys Chem, Biopolymer, Biophys Chem,Phys Chem Chem Phys, PLoS ONE, Proteins: Structure, Function and Bioinformatics, ProteinScience, Current Computer-Aided Drug Design, Genomics, Proteomics & BioinformaticsMember:American Chemical SocietyAssociate Faculty Member:Faculty of 1000 BiologyResearch grantsNIH R01 (Co-PI) 2012The Early Oligomer States of IAPP: Structure and Mechanism of Inhibition (Pending)Publications-Published (33 total, 2 in review; h-index16; total citations 1809)1. Sui W, Wu C, Li YQ (2000) Rapid simultaneous determination of four anthracene derivatives using asingle non-linear variable-angle synchronous fluorescence spectrum. Fresenius Journal of AnalyticalChemistry 368: 669-675.2. Sui W, Wu C, Li YQ, Wen WH (2001) Simultaneous determination of 1-chloroanthracene and 9-bromoanthracene by using matrix isopotential synchronous fluorescence spectrometry combinedwith derivative technique. Chinese Journal of Analytical Chemistry 29: 320-322.3. Li YQ, Sui W, Wu C, Yu LJ (2001) Derivative matrix isopotential synchronous fluorescence spectroscopyfor the direct determination of 1-hydroxypyrene as a urinary biomarker of exposure to polycyclicaromatic hydrocarbons. Anal Sci 17: 167-170.4. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong GM, et al. (2003) A point-charge force field for molecularmechanics simulations of proteins based on condensed-phase quantum mechanical calculations. JComput Chem 24: 1999-2012. Citation: 1074+5. Chowdhury S, Zhang W, Wu C, Xiong GM, Duan Y (2003) Breaking non-native hydrophobic clusters is therate-limiting step in the folding of an alanine-based peptide. Biopolymers 68: 63-75. Citation: 45+6. Wu C, Lei HX, Duan Y (2004) Formation of partially ordered oligomers of amyloidogenic hexapeptide(NFGAIL) in aqueous solution observed in molecular dynamics simulations. Biophys J 87: 3000-3009.Citation: 28+7. Zhang W, Wu C, Duan Y (2005) Convergence of replica exchange molecular dynamics. J Chem Phys 123:154105. Citation: 47+8. Wu C, Lei HX, Duan Y (2005) Elongation of ordered peptide aggregate of an amyloidogenic hexapeptideNFGAIL observed in molecular dynamics simulations with explicit solvent. J Am Chem Soc 127:13530-13537. Citation: 47+9. Wu C, Lei HX, Duan Y (2005) The role of Phe in the formation of well-ordered oligomers of amyloidogenichexapeptide ( NFGAIL) observed in molecular dynamics simulations with explicit solvent. Biophys J88: 2897-2906. Citation: 43+10. Wu C, Lei HX, Wang ZX, Zhang W, Duan Y (2006) Phenol red interacts with the protobril-like oligomersof an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts. BiophysJ 91: 3664-3672.11. Wang ZX, Zhang W, Wu C, Lei HX, Cieplak P, et al. (2006) Strike a balance: Optimization of backbonetorsion parameters of AMBER polarizable force field for simulations of proteins and peptides. JComput Chem 27: 781-790. Citation: 52+12. Lei HX, Wu C, Wang ZX, Duan Y (2006) Molecular dynamics simulations and free energy analyses onthe dimer formation of an amyloidogenic heptapeptide from human 2-microglobulin: Implication forthe protofibril structure. J Mol Biol 356: 1049-1063. Citation: 23+13. Wang ZX, Wu C, Lei HX, Duan Y (2007) Accurate ab initio study on the hydrogen-bond pairs in proteinsecondary structures. J Chem Theory Comput 3: 1527-1537.14. Lei HX, Wu C, Liu HG, Duan Y (2007) Folding free-energy landscape of villin headpiece subdomain frommolecular dynamics simulations. Proc Natl Acad Sci U S A 104: 4925-4930. Citation: 95+15. Wu C, Wang ZX, Lei HX, Zhang W, Duan Y (2007) Dual binding modes of Congo red to amyloidprotofibril surface observed in molecular dynamics simulations. J Am Chem Soc 129: 1225-1232.Citation: 60+2

Curriculum VitaeChun Wu16. Wu C, Wang ZX, Lei HX, Duan Y, Bowers MT, et al. (2008) The Binding of Thioflavin T and Its NeutralAnalog BTA-1 to Protofibrils of the Alzheimer's Disease A(16-22) Peptide Probed by MolecularDynamics Simulations. J Mol Biol 384: 718-729. Citation: 36+17. Lei HX, Wu C, Wang ZX, Zhou YQ, Duan Y (2008) Folding processes of the B domain of protein A to thenative state observed in all-atom ab initio folding simulations. J Chem Phys 128: 235105.18. Dupuis NF, Wu C, Shea JE, Bowers MT (2009) Human Islet Amyloid Polypeptide Monomers FormOrdered -hairpins: A Possible Direct Amyloidogenic Precursor. J Am Chem Soc 131: 18283-18292.Citation: 33+19. Wu C, Biancalana M, Koide S, Shea JE (2009) Binding Modes of Thioflavin-T to the Single-Layer -Sheet of the Peptide Self-Assembly Mimics. J Mol Biol 394: 627-633. Citation: 21+20. Lei HX, Wang ZX, Wu C, Duan Y (2009) Dual folding pathways of an protein from all-atom ab initiofolding simulations. J Chem Phys 131: 165105.21. Wu C † , Murray MM † , Bernstein SL † , Condron MM, Bitan G, et al. (2009) The Structure of A42 C-Terminal Fragments Probed by a Combined Experimental and Theoretical Study. J Mol Biol 387:492-501. Citation: 31+22. Grabenauer M, Wu C, Soto P, Shea JE, Bowers MT (2010) Oligomers of the Prion Protein Fragment106-126 Are Likely Assembled from -Hairpins in Solution, and Methionine Oxidation InhibitsAssembly without Altering the Peptide's Monomeric Conformation. J Am Chem Soc 132: 532-539.23. Jiang JL, Wu YB, Wang ZX*, Wu C* (2010) Assessing the Performance of Popular Quantum Mechanicsand Molecular Mechanics Methods and Revealing the Sequence-Dependent Energetic FeaturesUsing 100 Tetrapeptide Models. J Chem Theory Comput 6: 1199-1209.24. Wu C, Shea JE (2010) On the Origins of the Weak Folding Cooperativity of a Designed UltrafastProtein FSD-1. PLoS Comput Biol 6: e1000998.25. Wu C, Bowers MT, Shea JE (2010) Molecular Structures of Quiescently Grown and Brain-DerivedPolymorphic Fibrils of the Alzheimer Amyloid A(9-40) Peptide: A Comparison to Agitated Fibrils.PLoS Comput Biol 6: e1000693.26. Dupuis NF, Wu C, Shea JE, Bowers MT (2011) The Amyloid Formation Mechanism in Human IAPP:Dimers Have -Strand Monomer-Monomer Interfaces. J Am Chem Soc 133: 7240-7243.Citation: 21+27. Wu C, Shea JE (2011) Coarse-grained models for protein aggregation. Curr Opin Struct Biol 21: 209-220.Citation: 23+28. Wu C, Bowers MT, Shea JE (2011) On the Origin of the Stronger Binding of PIB over Thioflavin T toProtofibrils of the Alzheimer Amyloid- Peptide: A Molecular Dynamics Study. Biophys J 100: 1316-1324.29. Gessel MM † , Wu C † , Li HY † , Bitan G, Shea JE, et al. (2012) A(39-42) Modulates A Oligomerization butNot Fibril Formation. Biochemistry 51: 108-117.Highlighted at the TACC website (Texas Advanced Computing Center):http://www.tacc.utexas.edu/news/feature-stories/2012/alzheimers-disease30. Wu C, Shea JE (2012) The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases:Insights from Fully Atomistic Simulations. In: Dokholyan N, editor. Biological and Medical Physics,Biomedical Engineering. Berlin: Springer. pp. 215-227.31. Wu C, Scott J, Shea JE (2012) Binding of Congo red to amyloid protofibrils of the Alzheimer Aβ 9-40peptide probed by molecular dynamics simulations. Biophys J 103: 550-557.32. Wang XQ † , Wu C † , Vu A, Shea JE, Dahlquist FW (2012) Computational and Experimental AnalysesReveal the Essential Roles of Inter-domain Linkers in the Biological Function of Chemotaxis HistidineKinase CheA. J Am Chem Soc 134(39), 16107-1611033. Lei HX*, Wang XF, Wu C* (2012) Early stage intercalation of doxorubicin to DNA fragments observed inmolecular dynamics binding simulations. J Mol Graph Model 38, 279-289† Contribute equally* Corresponding authorsPublications-In press/Submitted/In preparation34. Jiang JL, Wen MW, Wang ZX*, Wu C* (2012) How accurate are the popular PCM/GB continuumsolvation models for predictions of the hydration free energies of amino acid side-chain analogs?Submitted.3

Curriculum VitaeChun Wu35. Susa AC, Wu C, Sivas SL, Dupuis NF, Raleigh D, et al. (2012) Monomeric Insulin and Insulin B-chainInhibit Oligomer Formation by Human Islet Amyloid Polypeptide. Submitted.36. Wu C, Shea JE (2012) Structural basis for physiological and pathological activities of Islet AmyloidPolypeptide (IAPP) probed by all-atom replica exchange molecular dynamics simulations. Inpreparation.37. Bleiholder C, Do T, Wu C, Shea JE, Bowers MT (2012) Inhibition or promotion mechanism of A25-35aggregation by different ligands. In preparation.Oral & poster presentationInvited talks:1. Wu C, Shea JE& Bowers MT “Multiple binding sites of Alzheimer’s A 16-22 protofibril-oligomer by Thioflavin-Tand its neutral analog (BTA-1) observed in molecular dynamics simulations”, College of Chemistry andChemical Engineering, Graduate University of Chinese Academy of Science, Beijing, China, Feb. 20082. Wu C, Shea JE& Bowers MT “An introduction to protein and peptide aggregation”, 238th American ChemicalSociety National Meeting & Exposition, Washington, DC, USA, Aug. 20093. Wu C & Shea JE“ab initio folding of / protein by All-atom Molecular Dynamics”, 2 nd ITP internationalsymposium, Santa Barbara, USA, Nov. 20094. Wu C “Molecular dynamics simulations and applications”, Xiamen University, Xiamen, China, Dec. 20095. Wu C, Shea JE& Bowers MT “The Binding of Thioflavin-T and its Neutral Analog PIB to Cross-b-subunit of theAlzheimer Aβ9-40 peptide probed by Molecular Dynamics simulations”, College of Chemistry andChemical Engineering, Graduate University of Chinese Academy of Science, Beijing, China, Dec. 20096. Wu C, M Grabenauer, Bowers MT & Shea JE“Predicting structures of small non-amyloid and amyloid proteinsusing molecular dynamics simulation in implicit water”, Isolated Biomolecules and Biomolecular Interactions2010, Berlin, Jun. 20107. Wu C “Dye binding, folding and aggregation of amyloid peptides probed by all-atom molecular dynamics (MD)simulations ”, LSU, LA, Feb. 20118. Wu C “Probing and optimizing functional small molecules and bio-molecules by molecular dynamics (MD)simulations”, LSU, LA, Feb. 20119. Wu C “Development of AMBER protein force fields and bio-applications of all-atom molecular dynamicssimulations”, Hong Kong University of Science & Technology, Hong Kong, China, May. 201110. Wu C “Molecular dynamics (MD) simulations: a great opportunity for China”, Xiamen University, Xiamen, China,May. 201111. Wu C “Development of AMBER protein force fields and bio-applications of all-atom molecular dynamicssimulations”, College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy ofScience, Beijing, China, May. 201112. Wu C “Computational modeling (sequence-structure-dynamics): a great opportunity for China”, Beijing Instituteof Genomics, Chinese Academy of Science, Beijing, China, May. 201113. Wu C “Development of AMBER protein force fields and bio-applications of all-atom molecular dynamicssimulations”, Fudan University, Shanghai, China, May. 201114. Wu C “Development of AMBER protein force fields and bio-applications of all-atom molecular dynamicssimulations”, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, China, May.201115. Wu C, Dupuis NF, Bowers MT and Shea JE “Folding and dimerization of type 2 diabetes amyloid formingamylin peptide using molecular dynamics simulations: potential drug targets”, The 11 th NationalConference of Quantum Chemistry, Hefei, China, May. 2011Other oral presentations:1. Wu C, Sui W & Li YQ “Rapid simultaneous determination of four anthracene derivatives using a single nonlinearvariable-angle synchronous fluorescence spectrum”, Fifth Asian Conference on Analytical Sciences(ASIANALYSIS V), Xiamen, China, May. 19992. Wu C, Shea JE& Bowers MT “Lateral Growth Mechanism of Amyloid Protofibrils: A Theoretical Study”,Conference on Ion Chemistry and Mass Spectrometry, Lake Arrowhead, CA, Jan. 20083. Wu C, NF Dupuis, Shea JE& Bowers MT “Probing amylin by Ion Mobility Mass Spectrometry (IMMS) andReplica Exchange Molecular Dynamics (REMD)”, Conference on Ion Chemistry and Mass Spectrometry,Lake Arrowhead, CA, Jan. 20094

Curriculum VitaeChun Wu4. Wu C, Shea JE& Bowers MT “The binding of Thioflavin-T and its neutral anlog PIB to protofibrils of theAlzheimer A 9-40 peptide probed by molecular dynamics simulations”, 238th American Chemical SocietyNational Meeting & Exposition, Washington, DC, USA, Aug. 20095. Wu C & Shea JE“ab initio folding of / protein by All-atom Molecular Dynamics ”, 238th American ChemicalSociety National Meeting & Exposition, Washington, DC, USA, Aug. 20096. Wu C, Bowers MT & Shea JE“The binding of dyes and inhibitors to amyloid peptides”, Conference on IonChemistry and Mass Spectrometry, Lake Arrowhead, CA, Jan. 2011Poster:1. Lin ZG, Wu C, Tong Y. G., Zhao Y. B., Xu J. G. and Yang S. K. (1996) “Fast generation of three-DimensionalFluorescence Spectrum (TDFS) of single component from Its excitation and emission spectra offluorescence by a computational method” Proc. of the 5th Chin. Lumin Spectrosc Anal Conf. 31-322. Lin ZG, Wu C, Zhao Y. B., Tong Y. G., Xu J. G. and Yang S. K. (1996) “Signal-noise ratio enhancement by anaccumulating method in 3-dimensional fluorescence spectrometry “ Proc of the 5th Chin LuminSpectrosc Anal Conf . 36-373. Wu C & Duan Y.“Formation of partially-ordered oligomers of amyloidogenic hexapeptide (NFGAIL)”, JohnsHopkins Protein Folding Meeting, Coolfont W. VA., Mar. 20034. Wu C, Lei HX & Duan Y.“Elongation of Ordered Peptide Aggregate of an Amyloidogenic Hexapeptide (NFGAIL)”ACS meeting, Philadelphia PA, Aug. 20045. Wu C & Shea JE “Critical role played by the interface side-chains in destabilizing/stabilizing the protofibrilstructure of Amyloid -peptide”, Proteins folding Gordon Conference, Ventura, CA, Jan. 20086. Wu C & Shea JE “ab initio folding of / protein by Replica Exchange Molecular Dynamics (REMD)”, Gordenconference: Biological Molecules In The Gas Phase and In Solution, Tilton, NH, Jun. 20097. Wu C & Shea JE“ab initio folding of / protein by All-atom Molecular Dynamics ”, 5th Worldwide ChineseTheoretical and Computational Chemistry Conference, Xiamen, China, Dec. 20098. Wu C, Dupuis NF, Bowers MT & Shea JE “β-rich conformations of the Human Islet Amyloid PolypeptideMonomers as direct precursors for β-sheet Rich Dimers: Evidence from simulation and Ion Mobility MassSpectrometry”, Proteins folding Gordon Conference, Ventura, CA, Jan. 20109. Wu C, Shea JE& Bowers MT “The Binding of Thioflavin-T and its Neutral Analog PIB to Cross-β-subunit of theAlzheimer Aβ9-40 peptide probed by Molecular Dynamics simulations”, Conference on Ion Chemistry andMass Spectrometry, Lake Arrowhead, CA, Jan. 2010Teaching Experience2009-now Co-mentor Dr. WANG Xiaofeng on his post-doc research2011-now Co-mentor Mr. WEN Mingwei and Mr. LING Jianping on Ph.D. research2009-2011 Gave chemistry outreach lectures to local high schools in Santa Barbara and Ventura, CA2009-2011 Mentored Mr. Justin Scott on his undergraduate research2008-2011 Co-Mentored Mr. JIANG JingLiang on his Ph. D. research1999-2002 Incorporated the computer-controlled data acquisition interface (LabWorks II) into theundergraduate (honor) general/analytical chemistry labs (19 labs);Developed three lab experiments for the undergraduate (honor) general/analytical chemistryTaught undergraduate honor general chemistry lab sections for 2 semestersTaught undergraduate general chemistry reading sections for 1 semesterEvaluated student performance1997-1998 Taught undergraduate analytical chemistry reading sections for 1 semesterEvaluated student performance1997-1998 Mentored Mr. DENG Tao (undergraduate) on his graduation researchProgramming projects:• Parallel implementation of constant pH replica-exchange method (MPI, Fortran)• Implementation of group based angle, torsion constraints in sander of AMBER (Fortran 95)• Implementation of harmonic constraints in sander of AMBER (Fortran 95)• Transplanting grow-to-fit (G2F) module of side chain refinement in AMBER 7 into AMBER 9 (Fortran 95)• Integrating various of components (sequence alignment, homology modeling, loop building, side chainbuilding and structure refinement) for structure modeling (TCL, PERL, C language and Fortran)5

Curriculum VitaeChun Wu• Parallel implementation (multiple CPUs for multiple parallel replica simulations) of replica-exchangemethod into sander, PMEMD of AMBER 7, 8, 9 (MPI, Fortran, Fortran 95)• Parallel version of pair-wise clustering using disks across computing nodes for clustering millions ofstructures (MPI, Fortran)• Parallel implementation of “ Correction energy map(CMAP)” in sander of AMBER 9 (Fortran 95)• Implementation of AMBER crd file reading/writing plugin in VMD (C++)• Adding periodical boundary condition to H-bond analysis in ptraj of AMBER (C language)• Development of motor driver for non-linear variable-angle synchronous fluorescence spectrometer (Clanguage)• Development of FPATH, an experiment design program to optimize scanning route of non-linearvariable-angle synchronous fluorescence spectroscopy (Visual Basic)Computer cluster system administratorResearch group cluster (110 compute nodes) 1999-2006, Linux, ROCKS, SGE, SQL, protein modeling/MD/QM packagesComputing Experience• Computational biophysical chemistry: binding mode prediction, binding free energy calculation, force fielddevelopment, parallel code development of replica exchange molecular dynamics simulation, all-atommolecular dynamics simulations, NWCHEM, GAUSSIAN, AMBER, GROMACS• Chemometrics: principal components analysis, partial least square regression, clustering algorithms• Bioinformatics: side chain refinement, protein structure refinement• Computer science: parallel computing, machine learning algorithms, database• Experienced programmer: MPI, FORTRAN, C, C++, Matlab, SQL, TCL, PERL, Python• Cluster user( Used 10 million CPU hours) : Texas Advance Computing Center (5400 nodes), Shiraz cluster(440 CPUs), Genome Center of UC Davis, Biowolf cluster (128 nodes), University of Delaware, PittsburghSupercomputing Center (750 nodes)Analytical experimental ExperienceSpectroscopy: MS-IMS, ESI-MS, Circular Dichroism, Fluorescence, IR, UV-Vis, NMRChromatography: GC-MS, HPLCReferencesProf. Joan E. Shea, Dept. of Chem. & Biochem., UC Santa Barbara, CA 93106, (805) 893-5604shea@chem.ucsb.eduProf. Michael T. Bowers, Dept. of Chem. & Biochem., UC Santa Barbara, CA 93106, (805) 893-2893bowers@chem.ucsb.eduProf. Yong Duan, Genome Center and Dept. of Applied Science, UC Davis, CA 95616, (530) 754-7632duan@ucdavis.eduProf. Zhixiang Wang, College of Chem. and Chemical Engineering, Graduate University of Chinese Academyof Sciences, Beijing, China, 100049, +86 (10) 8825-6674zxwang@gucas.ac.cnProf. Yaoqun Li, Dept. of Chem., Xiamen University, Xiamen, China, 365001, +86 (592) 218-5875yqlig@xmu.edu.cn6